Reports are that firearms were thrown overboard:
http://www.jpost.com/Headlines/Article.aspx?id=177475
And I object to your phrasing:”why was it that IDF forces had guns to kill a bunch of passengers but no passenger, on a boat Israel thought had arms, had a gun to shoot the IDF?”
Hmmm, the Israelis had guns to protect the Israeli troops;they didn’t board with the intention of killing folks. If the Israelis had wanted to kill the passengers, the Israelis could have (1) ordered an air attack; (2) planted a mine under the ship (3) blasted the ship out of the water in other ways. All of THOSE actions wouldn’t have resulted in any injuries to their own troops. As this article indicates, by an AlJazeera cameraman, the Israelis did NOT fire until some of their troops were overpowered and taken below deck.
Unfortunately, if a boarded ship throws all of its arms overboard and never used them (the only guns ever fired were IDF guns, according to the JP), then it looks like the passengers were merely being civil and didn’t want to kill while IDF soldiers went on a killing spree.